Head and neck cancer is a common disease worldwide, and more than 40,000 cases are diagnosed annually in the United States. The five-year survival rate is roughly 50% and has not improved over two decades. This research project focuses on the development of a new cancer biomarker paradigm based on the global epigenetic status of head and neck tissues. In many laboratories, DNA methylation is being examined as a means for early diagnosis of cancer. Recently DNA hypomethylation has been found to be a promising biomarker for the more advanced and aggressive stages of cancer, and there is an urgent need for analytical tools that will sample comprehensively the abnormal "methylome" hidden within the vast landscape of DNA repeats, in addition to the abnormal methylome of promoter-associated CpG islands. This grant application focuses on the validation of a novel microarray-based approach for epigenetic biomarker discovery and cancer classification that is complementary to other methods currently in use. The new method is relatively simple and has the unique capability to sample the methylation status of the majority of DNA repeats, as well as gene promoters, generating very large data sets. We will perform microarray-based methylation profiling using a statistically meaningful set of tumor samples from head and neck cancer patients. In addition, we will utilize the microarray-generated methylation profile information to identify clinically relevant subtypes of head and neck cancer, using a variety of analytical approaches. We will refine a subtype classification algorithm by inclusion of additional datasets available for the same samples, including allele gains and loses revealed by array-CGH and HPV infection status, as well as relevant patient clinical data. We will use this new information to address urgent diagnostic and prognostic clinical needs for improved classification of head and neck cancers in relation to diagnosis of early developmental stages, assessment of aggressiveness, likelihood of metastasis, and risk of recurrence after surgery.